Hi Renyi. Even though your questions aren't aroma.affymetrix-specific, I'll send my responses to the aroma.affymetrix list in case others have the same questions.
Comments below. On 6-Dec-09, at 6:46 PM, Renyi Liu wrote: > Hi, Mark, > > Thanks again for helping me with my previous question on CDF file. I > have read your article on "Promoter 1.0R Tiling array analysis" and > would like to apply MAT normalization to my dataset. Again, my dataset > is from Arabidopsis and I need to create my own CDF file. For MAT > analysis, we need to put copy number of probes into the bpmap file > (and the CDF file). If you got a chance, I'd appreciate your help on a > couple of more questions: You may be able to use the BPMAP file for Arabidopsis from the MAT website: http://liulab.dfci.harvard.edu/MAT/Download.htm ... that would already have copy number in there. > (1) should I filter out probes with copy number >10? (their xMAN paper > states that they remove probes with copy number >10) Yes, that's what they do for the BPMAP files at the MAT website. > (2) for probes that map to multiple locations, how many entries need > to included? (i.e. should I just randomly choose one of the mapping > locations and put in startpos?). If multiple locations are included, > the total number of probes will be much larger than the original > affymetrix bpmap file. You would want to keep all of them I guess, except for the >10 hits that you've filtered. So, yes, you would end up with more probes than what you started with, but I'd expect that it wouldn't be *much* larger, since (at least for human) only a small percentages of probes map to multiple locations. > (3) for MeDIP-chip data, which normalization method is the best choice > in your opinion? We typically use MAT for normalization, but you might be interested is this comparison: http://www.biomedcentral.com/1471-2105/10/204 Hope that helps. Cheers, Mark > Many thanks, > > Renyi > > -- > ============================ > Renyi Liu, PhD > Assistant Professor > Department of Botany and Plant Sciences > 3109 Batchelor Hall > University of California, Riverside > Riverside, CA 92521 > Email: renyi....@ucr.edu > Phone: (951)827-3987 > Fax: (951)827-4437 ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en
